Знайомство з терміналом

Last updated on 2024-07-26 | Edit this page

Overview

Questions

  • What is a command shell and why would I use one?

Objectives

  • Пояснити, як термінал пов’язаний з клавіатурою, екраном, операційною системою та програмами користувача.
  • Пояснити, коли та чому інтерфейси командного рядка слід використовувати замість графічних інтерфейсів.

Попередні знання

Люди та комп’ютери зазвичай взаємодіють багатьма різними способами, наприклад за допомогою клавіатури та миші, сенсорного екрану або системи розпізнавання мови. Найбільш поширений спосіб взаємодії з персональними комп’ютерами називається графічний інтерфейс користувача (GUI - graphical user interface). За допомогою такого інтерфейсу ми надаємо комп’ютеру інструкції, обираючи дію у меню за допомогою миші.

Хоча візуальна допомога графічного інтерфейсу користувача робить інтуїтивним його вивчення, такий спосіб надсилання інструкцій до комп’ютера дуже погано масштабується. Уявіть наступну задачу: для бібліографічного пошуку вам необхідно скопіювати третій рядок з тисячі вхідних файлів з тисячі різних директорій та вставити усе це в один файл. Using a GUI, you would not only be clicking at your desk for several hours, but you could potentially also commit an error in the process of completing this repetitive task. Саме тут ми й скористаємося перевагами терміналу Unix. The Unix shell is both a command-line interface (CLI) and a scripting language, allowing such repetitive tasks to be done automatically and fast. With the proper commands, the shell can repeat tasks with or without some modification as many times as we want. З використанням терміналу приклад задачі з бібліографічним пошуком може бути вирішений за секунди.

Термінал

The shell is a program where users can type commands. With the shell, it’s possible to invoke complicated programs like climate modeling software or simple commands that create an empty directory with only one line of code. The most popular Unix shell is Bash (the Bourne Again SHell — so-called because it’s derived from a shell written by Stephen Bourne). Bash is the default shell on most modern implementations of Unix and in most packages that provide Unix-like tools for Windows. Note that ‘Git Bash’ is a piece of software that enables Windows users to use a Bash like interface when interacting with Git.

Using the shell will take some effort and some time to learn. While a GUI presents you with choices to select, CLI choices are not automatically presented to you, so you must learn a few commands like new vocabulary in a language you’re studying. However, unlike a spoken language, a small number of “words” (i.e. commands) gets you a long way, and we’ll cover those essential few today.

The grammar of a shell allows you to combine existing tools into powerful pipelines and handle large volumes of data automatically. Sequences of commands can be written into a script, improving the reproducibility of workflows.

In addition, the command line is often the easiest way to interact with remote machines and supercomputers. Familiarity with the shell is near essential to run a variety of specialized tools and resources including high-performance computing systems. As clusters and cloud computing systems become more popular for scientific data crunching, being able to interact with the shell is becoming a necessary skill. We can build on the command-line skills covered here to tackle a wide range of scientific questions and computational challenges.

Let’s get started.

When the shell is first opened, you are presented with a prompt, indicating that the shell is waiting for input.

BASH 

$

The shell typically uses $ as the prompt, but may use a different symbol. In the examples for this lesson, we’ll show the prompt as $. Most importantly, do not type the prompt when typing commands. Only type the command that follows the prompt. This rule applies both in these lessons and in lessons from other sources. Also note that after you type a command, you have to press the Enter key to execute it.

The prompt is followed by a text cursor, a character that indicates the position where your typing will appear. The cursor is usually a flashing or solid block, but it can also be an underscore or a pipe. You may have seen it in a text editor program, for example.

Note that your prompt might look a little different. In particular, most popular shell environments by default put your user name and the host name before the $. Such a prompt might look like, e.g.:

BASH 

nelle@localhost $

The prompt might even include more than this. Do not worry if your prompt is not just a short $. This lesson does not depend on this additional information and it should also not get in your way. The only important item to focus on is the $ character itself and we will see later why.

So let’s try our first command, ls, which is short for listing. This command will list the contents of the current directory:

BASH 

$ ls

OUTPUT 

Desktop     Downloads   Movies      Pictures
Documents   Library     Music       Public

Command not found

If the shell can’t find a program whose name is the command you typed, it will print an error message such as:

BASH 

$ ks

OUTPUT 

ks: command not found

This might happen if the command was mis-typed or if the program corresponding to that command is not installed.

Nelle’s Pipeline: A Typical Problem

Nelle Nemo, a marine biologist, has just returned from a six-month survey of the North Pacific Gyre, where she has been sampling gelatinous marine life in the Great Pacific Garbage Patch. She has 1520 samples that she’s run through an assay machine to measure the relative abundance of 300 proteins. She needs to run these 1520 files through an imaginary program called goostats.sh. In addition to this huge task, she has to write up results by the end of the month, so her paper can appear in a special issue of Aquatic Goo Letters.

If Nelle chooses to run goostats.sh by hand using a GUI, she’ll have to select and open a file 1520 times. If goostats.sh takes 30 seconds to run each file, the whole process will take more than 12 hours of Nelle’s attention. With the shell, Nelle can instead assign her computer this mundane task while she focuses her attention on writing her paper.

The next few lessons will explore the ways Nelle can achieve this. More specifically, the lessons explain how she can use a command shell to run the goostats.sh program, using loops to automate the repetitive steps of entering file names, so that her computer can work while she writes her paper.

As a bonus, once she has put a processing pipeline together, she will be able to use it again whenever she collects more data.

Для того, щоб досягти своєї мети, Неллі необхідно знати, як:

  • перейти до файла/каталогу
  • створити файл/каталог
  • перевірити довжину файлу
  • з’єднати команди разом
  • отримати набір файлів
  • iterate over files
  • запустити скрипт, що містить розроблений нею конвеєр

Key Points

  • Термінал - це програма, основним призначенням якої є читання команд і запуск інших програм.
  • У цьому уроці використовується Bash. Це термінал за замовчуванням у багатьох реалізаціях Unix.
  • Програми можна запускати у Bash шляхом введення команд у вікні командного рядка.
  • Основними перевагами терміналу є високе співвідношення кількості дій до кількості натискань клавіш, підтримка автоматизації повторюваних завдань, а також можливість доступу до віддалених машин.
  • A significant challenge when using the shell can be knowing what commands need to be run and how to run them.